The difference is that this version creates just one hash and fills it with data in compound keys (joined with $;, \034 by default). Your version created lots of sub-hashes, allocating memory for each one. Using an array is even faster though.

I once solved a problem like this by using XS to compile a shared object containing a packed C data structure with my data, along with accessor routines also written in C. Then at runtime the Perl code just loaded the shared-object to get access to the data. It was really, really fast but I doubt I'd do it again - Berkeley DB has pretty much solved this problem.